Recombinant proteins are used in a wide range of contexts, from bio-industrial applications where proteins are used in the manufacturing of a commercially useful product, such as a biofuel, to therapeutic applications where proteins are used to treat a disease or condition. The production of recombinant proteins is carried out in cells engineered to express such proteins at high levels and which are grown in large quantities, often in liquid culture. The process of developing a cell line that produces a recombinant protein in large quantities and is adapted to growth under conditions suitable for commercial scale production is lengthy. Often, initial development and screening of cell lines is performed in adherent culture until candidate high yield recombinant cell lines are identified and subsequently, further development is performed to optimize the candidate cell lines for large scale production in suspension culture. Additional time and effort is often required for recombinant proteins that are intended for therapeutic applications in humans, where safety considerations favor the development of cell lines adapted to grow in defined media, free of heterogeneous animal components. Thus, even after initial cell line development is complete, a further round of development and optimization is often required to generate a suitable recombinant cell line expressing high levels of the polypeptide of interest, that can be used for commercial production. This process is time consuming and inefficient as it requires multiple rounds of cell line development. There is a need for tools and streamlined processes that shorten the time it takes to develop a high yield recombinant cell line that is suitable for commercial production of proteins, especially therapeutic proteins.